I apologise for the really basic question. I've probably said this a million times now but I'm returning to this field after a long time and I keep confusing myself by mis-remembering or half-remembering things from the past and it's not helping me. It would be easier coming to the field from fresh i think. Anyhow...

As i remember it, sequence databases always store the forward strand of a DNA chromsome in the 5' to 3' direction.

A gene is read in the 3' to 5' direction and so its complementary strand in the 5' to 3' direction is the same as the mRNA transcript. So i thought if a gene was on the reverse strand of a DNA molecule then the forward strand in the 5' to 3' direction gives the sequence on the corresponding mRNA (ignoring introns for simplicity).

However I'm just looking at a gene now in ensembl and this gene is described as being on the forward strand. If you look at the forward strand it contains the exact same sequence as the gene's mRNA. So to me then, if the mRNA runs on the forward strand in the 5' to 3' direction the actual gene is on the reverse strand is it not?

Is this a convention issue that I have mis-remembered? Is a gene classed as being on the forward strand if its mRNA sequence is 'on' the forward strand.

Sounds like you're trying to knit a few hazy concepts together too quickly - it might help to start by completely ignoring the RNA polymerase (the machinery that does the transcription in the "opposite" direction), and building up your understanding from scratch. Here is a stab at an explanation, hopefully it won't make things worse!

Start with the basics:

DNA is double-stranded. By convention, for a reference chromosome, one whole strand is designated the "forward strand" and the other the "reverse strand". This designation is arbitrary. Sometimes the terms "plus strand" and "minus strand" are used instead.

Visually (I'm not talking about the transcription machinery yet), you would typically read the sequence of a strand in the 5-3 direction. For the forward strand, this means reading left-to-right, and for the reverse strand it means right-to-left.

A gene can live on a DNA strand in one of two orientations. The gene is said to have a coding strand (also known as its sense strand), and a template strand (also known as its antisense strand). For 50% of genes, its coding strand will correspond to the chromosome's forward strand, and for the other 50% it will correspond to the reverse strand.

The mRNA (and protein) sequence of a gene corresponds to the DNA sequence as read (again, visually) from the gene's coding strand. So the mRNA sequence always corresponds to the 5-3 coding sequence of a gene.

Now, the RNA polymerase machinery moves along the DNA in the 5-3 orientation of the coding strand (e.g. left-to-right for a forward strand gene). It reads the bases from the template strand (so it is reading in the 3-5 direction from the point-of-view of the template strand), and builds the mRNA as it goes. This means that the mRNA matches the coding sequence of the gene, not the template sequence. (This diagram from Wikipedia illustrates).

Annotations such as Ensembl and UCSC are concerned with the coding sequences of genes, so when they say a gene is on the forward strand, it means the gene's coding sequence is on the forward strand. To follow through again, that means that during transcription of this forward-strand gene, the gene's template sequence is read from the reverse strand, producing an mRNA that matches the sequence on the forward strand.

Fair enough, I guess the answer is "yes" then :) I partially used the answer to clarify things in my own head too. I can understand why you consider the template strand to be "actual" gene, but I would always have conceptualised it as the other way around (feels easier to me anyway). Things must get interesting in your view when you consider anti-sense transcription :)

@Bio_X2Y : Your first mention that the designation of forward and reverse strands is arbitrary. Are you sure about this ?
I imagined that the forward strand was the one with the 5' end closest to centromere, no ?

Quote: "the RNA polymerase machinery moves along the DNA in the 5-3 orientation of the coding strand ... and builds the cDNA as it goes."
Not trying to be obtuse here, but doesn't the RNAP make RNA which would be complementary to the template?
Quote: "This means that the cDNA matches the coding sequence of the gene, not the template sequence."
I would have thought that the cDNA, which is complementary to the mRNA (and coding sequence), is identical to the template, and not the coding sequence.
Am I thinking about this wrong?

Short answer - yes. A "gene" is on the forward strand if its mRNA is on the forward strand.

I placed quotation marks around "gene" because, perhaps surprisingly, it is not a very useful word. In the context of this question we're using "sequence of a gene" to mean the same as "sequence of the mRNA transcribed from the gene." So we're referring to the same strand because we're talking about the same object.

What is a gene though? Most "genes" give rise to multiple transcripts. So we might say a gene is a region of DNA that serves as a template for transcription. A gene is not really a single object with start and end. It will have a "minimum start" (the 5'-most base from which transcription occurs) and a "maximum end" (the 3'-most base at which transcription terminates). So perhaps it's best to forget about genes and think about transcripts and their properties.

I agree that the "start < end" convention takes some getting used to but it makes a lot of sense when it comes to performing range calculations with sequences. If you just name the strands "+" or "-" and set start < end, you can forget about all the other terminology (forward/reverse, 5'/3' and so on), it all "just works".

I don't think i follow what your point is. Bio_x2y has confirmed for me what I thought about template and coding strands.

I think what you are talking about is another conventions issue whereby the start of a gene is always less than end of a gene even if you are on the reverse strand. On the reverse strand the start of the coding strand is higher than the end if you are using the 5' end of the forward strand as base 1. But by convention you give the gene coordinates so start is always less than the end (and flip the start and end coordinates in your transformations)

Personally i've always thought it looks a bit odd when you see a gene on the reverse strand and the start position of its second exon is lower than the end positon of its previous exon. I gues you just get used to reading from right to left for reverse strand stuff